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- PDB-7ob5: Crystal structure of 14-3-3 sigma in complex with LDB1 phosphopeptide -

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Basic information

Entry
Database: PDB / ID: 7ob5
TitleCrystal structure of 14-3-3 sigma in complex with LDB1 phosphopeptide
Components
  • 14-3-3 protein sigma
  • LDB1 phosphopeptide
KeywordsSIGNALING PROTEIN / 14-3-3 sigma protein-peptide complex
Function / homology
Function and homology information


Expression and translocation of olfactory receptors / regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / beta-catenin-TCF complex / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / epithelial structure maintenance / LIM domain binding ...Expression and translocation of olfactory receptors / regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / beta-catenin-TCF complex / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / epithelial structure maintenance / LIM domain binding / gastrulation with mouth forming second / Cardiogenesis / anterior/posterior axis specification / regulation of focal adhesion assembly / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / cell leading edge / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / somatic stem cell population maintenance / Activation of BAD and translocation to mitochondria / phosphoserine residue binding / hair follicle development / negative regulation of keratinocyte proliferation / establishment of skin barrier / negative regulation of protein localization to plasma membrane / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein localization / positive regulation of cell adhesion / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / regulation of cell migration / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / transcription coregulator activity / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of transcription elongation by RNA polymerase II / Regulation of expression of SLITs and ROBOs / Wnt signaling pathway / neuron differentiation / intrinsic apoptotic signaling pathway in response to DNA damage / intracellular protein localization / nervous system development / regulation of protein localization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cell growth / transcription regulator complex / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription coactivator activity / regulation of cell cycle / cell adhesion / cadherin binding / negative regulation of DNA-templated transcription / chromatin binding / protein kinase binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular space / DNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
LIM-domain binding protein/SEUSS / LIM interaction domain / LIM-domain binding protein / LIM interaction domain (LID) / LIM interaction domain (LID) domain profile. / 14-3-3 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein ...LIM-domain binding protein/SEUSS / LIM interaction domain / LIM-domain binding protein / LIM interaction domain (LID) / LIM interaction domain (LID) domain profile. / 14-3-3 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein
Similarity search - Domain/homology
14-3-3 protein sigma / LIM domain-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCentorrino, F. / Andlovic, B. / Ottmann, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission675179European Union
CitationJournal: Cell Chem Biol / Year: 2023
Title: IFN alpha primes cancer cells for Fusicoccin-induced cell death via 14-3-3 PPI stabilization.
Authors: Andlovic, B. / Heilmann, G. / Ninck, S. / Andrei, S.A. / Centorrino, F. / Higuchi, Y. / Kato, N. / Brunsveld, L. / Arkin, M. / Menninger, S. / Choidas, A. / Wolf, A. / Klebl, B. / Kaschani, ...Authors: Andlovic, B. / Heilmann, G. / Ninck, S. / Andrei, S.A. / Centorrino, F. / Higuchi, Y. / Kato, N. / Brunsveld, L. / Arkin, M. / Menninger, S. / Choidas, A. / Wolf, A. / Klebl, B. / Kaschani, F. / Kaiser, M. / Eickhoff, J. / Ottmann, C.
History
DepositionApr 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein sigma
P: LDB1 phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7167
Polymers29,4842
Non-polymers2325
Water7,386410
1
A: 14-3-3 protein sigma
P: LDB1 phosphopeptide
hetero molecules

A: 14-3-3 protein sigma
P: LDB1 phosphopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,43114
Polymers58,9674
Non-polymers46410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5430 Å2
ΔGint-63 kcal/mol
Surface area23910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.590, 112.188, 62.573
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-301-

CA

21A-792-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AP

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 28226.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31947
#2: Protein/peptide LDB1 phosphopeptide / LIM domain-binding protein 1 / LDB-1 / Carboxyl-terminal LIM domain-binding protein 2 / CLIM-2 / ...LIM domain-binding protein 1 / LDB-1 / Carboxyl-terminal LIM domain-binding protein 2 / CLIM-2 / LIM domain-binding factor CLIM2 / hLdb1 / Nuclear LIM interactor


Mass: 1257.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q86U70

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Non-polymers , 5 types, 415 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.095 M Hepes pH 7.1, 28% PEG 400, 0.19 M CaCl2 and 5 % Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5419 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.8→41.31 Å / Num. obs: 27183 / % possible obs: 99.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 10.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Net I/σ(I): 19.7
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 6.7 / Num. unique obs: 1280 / CC1/2: 0.962 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JC3

4jc3


Resolution: 1.8→41.3 Å / SU ML: 0.1227 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.2016 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1708 1359 5 %
Rwork0.1383 25808 -
obs0.14 27167 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.87 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 10 410 2335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812091
X-RAY DIFFRACTIONf_angle_d0.90812838
X-RAY DIFFRACTIONf_chiral_restr0.0448308
X-RAY DIFFRACTIONf_plane_restr0.0056381
X-RAY DIFFRACTIONf_dihedral_angle_d15.18211307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.870.18891300.15792461X-RAY DIFFRACTION96.79
1.87-1.940.22571340.14592556X-RAY DIFFRACTION99.7
1.94-2.030.18641340.14382561X-RAY DIFFRACTION100
2.03-2.140.16451360.132553X-RAY DIFFRACTION100
2.14-2.270.16111340.12292565X-RAY DIFFRACTION100
2.27-2.440.15831360.11892566X-RAY DIFFRACTION100
2.44-2.690.17791360.13222593X-RAY DIFFRACTION100
2.69-3.080.17651360.14172587X-RAY DIFFRACTION100
3.08-3.880.16151390.12862639X-RAY DIFFRACTION100
3.88-41.30.15921440.16132727X-RAY DIFFRACTION99.9

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